[R-sig-eco] EcologicalNicheModellingUsingR_ NeftaliSillero_UK_16-20October

Wed Feb 1 13:01:27 CET 2017

Ecological niche modelling using R (ENMR01)

Delivered by Dr. Neftali Sillero

http://www.prstatistics.com/course/ecological-niche-modelling-using-r-enmr01/

This course will run from 16th – 20th October 2017 at SCENE field 
station, Loch Lomond national park, Scotland

The course will cover the base theory of ecological niche modelling and 
its main methodologies. By the end of this 5-day practical course, 
attendees will have the capacity to perform ecological niche models and 
understand their results, as well as to choose and apply the correct 
methodology depending on the aim of their type of study and data.

Ecological niche, species distribution, habitat distribution, or 
climatic envelope models are different names for similar mechanistic or 
correlative models, empirical or mathematical approaches to the 
ecological niche of a species, where different types of ecogeographical 
variables (environmental, topographical, human) are related with a 
species physiological data or geographical locations, in order to 
identify the factors limiting and defining the species' niche. ENMs have 
become popular due to the need for efficiency in the design and 
implementation of conservation management.

The course will be mainly practical, with some theoretical lectures. All 
modelling processes and calculations will be performed with R, the free 
software environment for statistical computing and graphics 
(http://www.r-project.org/). Attendees will learn to use modelling 
algorithms like Maxent, Bioclim, Domain, and logistic regressions, and R 
packages for computing ENMs like Dismo and Biomod2. Also, students will 
learn to compare different ecological niche models using the Ecospat 
package.

Course content is as follows

Monday 16th – Classes from 09:00 to 17:00
Elementary concepts on Ecological Niche Modelling
Module 1: Introduction to ENM theory. Definition of ecological niche 
model; introduction to species ecological niche theory, types of 
ecological niches, types of ENM, diagram BAM, ENMs as approximations to 
species’ niches.
Module 2: Problems and limitations on ENM. Assumptions and 
uncertainties, equilibrium concept, niche conservatism, autocorrelation 
and intensity, sample size, correlation of environmental variables, size 
and form of study area, thresholds, model validation, model projections.
Module 3: Methods on ENM. Mechanistic and correlative models. Overlap 
Analysis, Biomod, Domain, Habitat, Distance of Mahalanobis, ENFA, GARP, 
Maxent, Logistic regression, Generalised Linear Models, Generalised 
Additive Models, Generalised Boosted Regression Models, Random Forest, 
Support Vector Machines, Artificial Neural Network.
Module 4: Conceptual and practice steps to calculate ENM. How to make an 
ENM step-by-step.
Module 5: Applications of ENM. Ecological niche identification, 
Identification of contact zones, Integration with genetical data, 
Species expansions, Species invasions, Dispersion hypotheses, Species 
conservation status, Prediction of future conservation problems, 
Projection to future and past climate change scenarios, Modelling past 
species, Modelling species richness, Road-kills, Diseases, Windmills, 
Location of protected areas.

Tuesday 17th – Classes from 09:00 to 17:00
Prepare environmental variables and run ecological niche models with 
dismo package.
Module 6: Preparing variables. Choosing environmental data sources, 
Downloading variables, Clipping variables, Aggregating variables, 
Checking pixel size, Checking raster limits, Checking NoData, 
Correlating variables.
Module 7: Dismo practice. How to run an ENM using the R package dismo.

Wednesday 18th – Classes from 09:00 to 17:00
Run ecological niche models with Biomod2 package and Maxent.
Module 8: Biomod2 practice. How to run an ENM using the R package 
Biomod2.
Module 9: Maxent practice. How to run an ENM using the R packages dismo 
and Biomod2 as well as Maxent software.

Thursday 19th – Classes from 09:00 to 17:00
Compare ecological niche models with ecospat.
Module 10: Ecospat practice. Compare statistically two different 
ecological niche models using the R package Ecospat.
Module 11: Students’ talks. Attendees will have the opportunity to 
present their own data and analyse which is the best way to successfully 
obtain an ENM.

Friday 20th – Classes from 09:00 to 17:00
Run ecological niche models with your own data.
Module 12: Final practical. In this practical, the students will run ENM 
with their own data or with a new dataset, applying all the methods 
showed during the previous days.

Please email any inquiries to oliverhooker at prstatistics.com or visit our 
website www.prstatistics.com

Please feel free to distribute this material anywhere you feel is 
suitable

Our other courses

1.	ADVANCED PYTHON FOR BIOLOGISTS (February 2017) #APYB
http://www.prstatistics.com/course/advanced-python-biologists-apyb01/

2.	STABLE ISOTOPE MIXING MODELS USING SIAR, SIBER AND MIXSIAR USING R 
(February 2017) #SIMM
http://www.prstatistics.com/course/stable-isotope-mixing-models-using-r-simm03/

3.	NETWORK ANAYLSIS FOR ECOLOGISTS USING R (March 2017) #NTWA
http://www.prstatistics.com/course/network-analysis-ecologists-ntwa01/

4.	ADVANCES IN MULTIVARIATE ANALYSIS OF SPATIAL ECOLOGICAL DATA (April 
2017) #MVSP
http://www.prstatistics.com/course/advances-in-spatial-analysis-of-multivariate-ecological-data-theory-and-practice-mvsp02/

5.	INTRODUCTION TO STATISTICS AND R FOR BIOLOGISTS (April 2017) #IRFB
http://www.prstatistics.com/course/introduction-to-statistics-and-r-for-biologists-irfb02/

6.	ADVANCING IN STATISTICAL MODELLING USING R (April 2017) #ADVR
http://www.prstatistics.com/course/advancing-statistical-modelling-using-r-advr05/

7.	GEOMETRIC MORPHOMETRICS USING R (June 2017) #GMMR
http://www.prstatistics.com/course/geometric-morphometrics-using-r-gmmr01/

8.	MULTIVARIATE ANALYSIS OF SPATIAL ECOLOGICAL DATA (June 2017) #MASE
http://www.prstatistics.com/course/multivariate-analysis-of-spatial-ecological-data-using-r-mase01/

9.	TIME SERIES MODELS FOR ECOLOGISTS USING R (JUNE 2017 (#TSME)

10.	BIOINFORMATICS FOR GENETICISTS AND BIOLOGISTS (July 2017) #BIGB
http://www.prstatistics.com/course/bioinformatics-for-geneticists-and-biologists-bigb02/

11.	SPATIAL ANALYSIS OF ECOLOGICAL DATA USING R (August 2017) #SPAE
http://www.prstatistics.com/course/spatial-analysis-ecological-data-using-r-spae05/

12.	ECOLOGICAL NICHE MODELLING (October 2017) #ENMR
http://www.prstatistics.com/course/ecological-niche-modelling-using-r-enmr01/

13.	INTRODUCTION TO BIOINFORMATICS USING LINUX (October 2017) #IBUL
http://www.prstatistics.com/course/introduction-to-bioinformatics-using-linux-ibul02/

14.	STRUCTURAL EQUATION MODELLING FOR ECOLOGISTS AND EVOLUTIONARY 
BIOLOGISTS (October 2017) #SEMR

15.	GENETIC DATA ANALYSIS USING R (October 2017 TBC) #GDAR

16.	LANDSCAPE (POPULATION) GENETIC DATA ANALYSIS USING R (November 2017 
TBC) #LNDG
http://www.prstatistics.com/course/landscape-genetic-data-analysis-using-r-lndg02/

17.	APPLIED BAYESIAN MODELLING FOR ECOLOGISTS AND EPIDEMIOLOGISTS 
(November 2017) #ABME
http://www.prstatistics.com/course/applied-bayesian-modelling-ecologists-epidemiologists-abme03/

18.	INTRODUCTION TO METHODS FOR REMOTE SENSING (November 2017) #IRMS

19.	INTRODUCTION TO PYTHON FOR BIOLOGISTS (November 2017) #IPYB
http://www.prstatistics.com/course/introduction-to-python-for-biologists-ipyb04/

20.	DATA VISUALISATION AND MANIPULATION USING PYTHON (December 2017) 
#DVMP
http://www.prstatistics.com/course/data-visualisation-and-manipulation-using-python-dvmp01/

21.	ADVANCING IN STATISTICAL MODELLING USING R (December 2017) #ADVR
http://www.prstatistics.com/course/advancing-statistical-modelling-using-r-advr07/

22.	INTRODUCTION TO BAYESIAN HIERARCHICAL MODELLING (January 2018) #IBHM
http://www.prstatistics.com/course/introduction-to-bayesian-hierarchical-modelling-using-r-ibhm02/

23.	PHYLOGENETIC DATA ANALYSIS USING R (TBC) #PHYL

Oliver Hooker PhD.
PR statistics
3/1
128 Brunswick Street
Glasgow
G1 1TF
+44 (0) 7966500340
www.prstatistics.com
www.prstatistics.com/organiser/oliver-hooker/